1. Filter detection by area

• Using the script select_biggest.groovy, you can filter the nuclei by area to keep the top N% biggest.
• To use the script, you just have to open it in your script editor, edit the settings and run it.
• The settings are as follows:
  • Line 11 (source_annotations): The list of polygons into which you have your detections. For example, if you segmented some nuclei in polygons of tumor and want to filter them, you should have ["Tumor"] as value. If you have several types of polygons, you can add as many classes as you need ["Tumor", "MySuperClass"].
  • Line 12 (percentage): The percentage of objects that will be conserved after they were sorted by area. Percentage is a number between 0 (0.00%) and 1 (100.0%).
  • Line 13 (use_cell): If your detections are cells (expanded nuclei) you can pass this to true to base the area on the cell's area rather than the nucleus' area.
• After the script execution is over, the biggest nuclei will have a new class representing their status of "top-N%".

2. Multiplex classification